Title: “Differential Expression Identification”
Purpose: “ASPIS omics Steatosis case study”
Input.data: “NormData_TG_Gates_Hum_invitro_ENS.txt”
Author: “Marcha Verheijen (ONTOX)”
Date: ‘2024-01-11’

Applied tools:

The R-ODAF pipeline (Omics Data Analysis Framework for Regulatory Application)

for Microarray technology was used. (Publication: “R-ODAF: Omics data analysis framework for regulatory application”, 2022, Regulatory Toxicology and Pharmacology.) This pipeline can be found at https://github.com/R-ODAF/Main and was based on:

ArrayAnalysis - affyAnalysisStat

a tool for statistical analysis of Affymetrix expression data. Copyright 2010-2014 BiGCaT Bioinformatics

Overview of samples and groups

Overview of array names and array groups
Array Name CompoundClass Group Group_Dose SteatosisPotential Group_Time CompoundName DoseGroup Treatment TimeDose TimeDose_low TimeDose_middle TimeDose_high TimeDose2 TimeDose_middlehigh DoseValue DoseUnit Time TimeUnit
003016027024.CEL TG_hum_vit_Ami_ctl_2h_1 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_2h amiodarone_Control Control none Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control NA 2 hour
003016027025.CEL TG_hum_vit_Ami_ctl_2h_2 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_2h amiodarone_Control Control none Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control NA 2 hour
003016028006.CEL TG_hum_vit_Ami_ctl_8h_1 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_8h amiodarone_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016028007.CEL TG_hum_vit_Ami_ctl_8h_2 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_8h amiodarone_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016028014.CEL TG_hum_vit_Ami_ctl_24h_1 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_24h amiodarone_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016028015.CEL TG_hum_vit_Ami_ctl_24h_2 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_24h amiodarone_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016027026.CEL TG_hum_vit_Ami_280nm_2h_1 Steatotic Steatotic Steatotic_Low low Steatotic_2h amiodarone_Low Low amiodarone Steatotic_2h_Low Steatotic_2h_Low Steatotic_2h_Low 0.28 micromolar 2 hour
003016028001.CEL TG_hum_vit_Ami_280nm_2h_2 Steatotic Steatotic Steatotic_Low low Steatotic_2h amiodarone_Low Low amiodarone Steatotic_2h_Low Steatotic_2h_Low Steatotic_2h_Low 0.28 micromolar 2 hour
003016028008.CEL TG_hum_vit_Ami_280nm_8h_1 Steatotic Steatotic Steatotic_Low low Steatotic_8h amiodarone_Low Low amiodarone Steatotic_8h_Low Steatotic_8h_Low Steatotic_8h_Low 0.28 micromolar 8 hour
003016028009.CEL TG_hum_vit_Ami_280nm_8h_2 Steatotic Steatotic Steatotic_Low low Steatotic_8h amiodarone_Low Low amiodarone Steatotic_8h_Low Steatotic_8h_Low Steatotic_8h_Low 0.28 micromolar 8 hour
003016028016.CEL TG_hum_vit_Ami_280nm_24h_1 Steatotic Steatotic Steatotic_Low low Steatotic_24h amiodarone_Low Low amiodarone Steatotic_24h_Low Steatotic_24h_Low Steatotic_24h_Low 0.28 micromolar 24 hour
003016028017.CEL TG_hum_vit_Ami_280nm_24h_2 Steatotic Steatotic Steatotic_Low low Steatotic_24h amiodarone_Low Low amiodarone Steatotic_24h_Low Steatotic_24h_Low Steatotic_24h_Low 0.28 micromolar 24 hour
003016028002.CEL TG_hum_vit_Ami_1400nm_2h_1 Steatotic Steatotic Steatotic_Middle middle Steatotic_2h amiodarone_Middle Middle amiodarone Steatotic_2h_Middle Steatotic_2h_Middle Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 1.40 micromolar 2 hour
003016028003.CEL TG_hum_vit_Ami_1400nm_2h_2 Steatotic Steatotic Steatotic_Middle middle Steatotic_2h amiodarone_Middle Middle amiodarone Steatotic_2h_Middle Steatotic_2h_Middle Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 1.40 micromolar 2 hour
003016028010.CEL TG_hum_vit_Ami_1400nm_8h_1 Steatotic Steatotic Steatotic_Middle middle Steatotic_8h amiodarone_Middle Middle amiodarone Steatotic_8h_Middle Steatotic_8h_Middle Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 1.40 micromolar 8 hour
003016028011.CEL TG_hum_vit_Ami_1400nm_8h_2 Steatotic Steatotic Steatotic_Middle middle Steatotic_8h amiodarone_Middle Middle amiodarone Steatotic_8h_Middle Steatotic_8h_Middle Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 1.40 micromolar 8 hour
003016028018.CEL TG_hum_vit_Ami_1400nm_24h_1 Steatotic Steatotic Steatotic_Middle middle Steatotic_24h amiodarone_Middle Middle amiodarone Steatotic_24h_Middle Steatotic_24h_Middle Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 1.40 micromolar 24 hour
003016028019.CEL TG_hum_vit_Ami_1400nm_24h_2 Steatotic Steatotic Steatotic_Middle middle Steatotic_24h amiodarone_Middle Middle amiodarone Steatotic_24h_Middle Steatotic_24h_Middle Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 1.40 micromolar 24 hour
003016028004.CEL TG_hum_vit_Ami_7um_2h_1 Steatotic Steatotic Steatotic_High high Steatotic_2h amiodarone_High High amiodarone Steatotic_2h_High Steatotic_2h_High Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 7.00 micromolar 2 hour
003016028005.CEL TG_hum_vit_Ami_7um_2h_2 Steatotic Steatotic Steatotic_High high Steatotic_2h amiodarone_High High amiodarone Steatotic_2h_High Steatotic_2h_High Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 7.00 micromolar 2 hour
003016028012.CEL TG_hum_vit_Ami_7um_8h_1 Steatotic Steatotic Steatotic_High high Steatotic_8h amiodarone_High High amiodarone Steatotic_8h_High Steatotic_8h_High Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 7.00 micromolar 8 hour
003016028013.CEL TG_hum_vit_Ami_7um_8h_2 Steatotic Steatotic Steatotic_High high Steatotic_8h amiodarone_High High amiodarone Steatotic_8h_High Steatotic_8h_High Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 7.00 micromolar 8 hour
003016028020.CEL TG_hum_vit_Ami_7um_24h_1 Steatotic Steatotic Steatotic_High high Steatotic_24h amiodarone_High High amiodarone Steatotic_24h_High Steatotic_24h_High Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 7.00 micromolar 24 hour
003016028021.CEL TG_hum_vit_Ami_7um_24h_2 Steatotic Steatotic Steatotic_High high Steatotic_24h amiodarone_High High amiodarone Steatotic_24h_High Steatotic_24h_High Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 7.00 micromolar 24 hour
003016018004.CEL TG_hum_vit_Ctc_ctl_2h_1 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_2h carbon tetrachloride_Control Control none Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control NA 2 hour
003016018005.CEL TG_hum_vit_Ctc_ctl_2h_2 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_2h carbon tetrachloride_Control Control none Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control NA 2 hour
003016018012.CEL TG_hum_vit_Ctc_ctl_8h_1 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_8h carbon tetrachloride_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016018013.CEL TG_hum_vit_Ctc_ctl_8h_2 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_8h carbon tetrachloride_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016018020.CEL TG_hum_vit_Ctc_ctl_24h_1 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_24h carbon tetrachloride_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016018021.CEL TG_hum_vit_Ctc_ctl_24h_2 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_24h carbon tetrachloride_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016018006.CEL TG_hum_vit_Ctc_300um_2h_1 Steatotic Steatotic Steatotic_Low low Steatotic_2h carbon tetrachloride_Low Low carbon tetrachloride Steatotic_2h_Low Steatotic_2h_Low Steatotic_2h_Low 300.00 micromolar 2 hour
003016018007.CEL TG_hum_vit_Ctc_300um_2h_2 Steatotic Steatotic Steatotic_Low low Steatotic_2h carbon tetrachloride_Low Low carbon tetrachloride Steatotic_2h_Low Steatotic_2h_Low Steatotic_2h_Low 300.00 micromolar 2 hour
003016018014.CEL TG_hum_vit_Ctc_300um_8h_1 Steatotic Steatotic Steatotic_Low low Steatotic_8h carbon tetrachloride_Low Low carbon tetrachloride Steatotic_8h_Low Steatotic_8h_Low Steatotic_8h_Low 300.00 micromolar 8 hour
003016018015.CEL TG_hum_vit_Ctc_300um_8h_2 Steatotic Steatotic Steatotic_Low low Steatotic_8h carbon tetrachloride_Low Low carbon tetrachloride Steatotic_8h_Low Steatotic_8h_Low Steatotic_8h_Low 300.00 micromolar 8 hour
003016018022.CEL TG_hum_vit_Ctc_300um_24h_1 Steatotic Steatotic Steatotic_Low low Steatotic_24h carbon tetrachloride_Low Low carbon tetrachloride Steatotic_24h_Low Steatotic_24h_Low Steatotic_24h_Low 300.00 micromolar 24 hour
003016018023.CEL TG_hum_vit_Ctc_300um_24h_2 Steatotic Steatotic Steatotic_Low low Steatotic_24h carbon tetrachloride_Low Low carbon tetrachloride Steatotic_24h_Low Steatotic_24h_Low Steatotic_24h_Low 300.00 micromolar 24 hour
003016018008.CEL TG_hum_vit_Ctc_1500um_2h_1 Steatotic Steatotic Steatotic_Middle middle Steatotic_2h carbon tetrachloride_Middle Middle carbon tetrachloride Steatotic_2h_Middle Steatotic_2h_Middle Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 1500.00 micromolar 2 hour
003016018009.CEL TG_hum_vit_Ctc_1500um_2h_2 Steatotic Steatotic Steatotic_Middle middle Steatotic_2h carbon tetrachloride_Middle Middle carbon tetrachloride Steatotic_2h_Middle Steatotic_2h_Middle Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 1500.00 micromolar 2 hour
003016018016.CEL TG_hum_vit_Ctc_1500um_8h_1 Steatotic Steatotic Steatotic_Middle middle Steatotic_8h carbon tetrachloride_Middle Middle carbon tetrachloride Steatotic_8h_Middle Steatotic_8h_Middle Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 1500.00 micromolar 8 hour
003016018017.CEL TG_hum_vit_Ctc_1500um_8h_2 Steatotic Steatotic Steatotic_Middle middle Steatotic_8h carbon tetrachloride_Middle Middle carbon tetrachloride Steatotic_8h_Middle Steatotic_8h_Middle Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 1500.00 micromolar 8 hour
003016018024.CEL TG_hum_vit_Ctc_1500um_24h_1 Steatotic Steatotic Steatotic_Middle middle Steatotic_24h carbon tetrachloride_Middle Middle carbon tetrachloride Steatotic_24h_Middle Steatotic_24h_Middle Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 1500.00 micromolar 24 hour
003016018025.CEL TG_hum_vit_Ctc_1500um_24h_2 Steatotic Steatotic Steatotic_Middle middle Steatotic_24h carbon tetrachloride_Middle Middle carbon tetrachloride Steatotic_24h_Middle Steatotic_24h_Middle Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 1500.00 micromolar 24 hour
003016018010.CEL TG_hum_vit_Ctc_7500um_2h_1 Steatotic Steatotic Steatotic_High high Steatotic_2h carbon tetrachloride_High High carbon tetrachloride Steatotic_2h_High Steatotic_2h_High Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 7500.00 micromolar 2 hour
003016018011.CEL TG_hum_vit_Ctc_7500um_2h_2 Steatotic Steatotic Steatotic_High high Steatotic_2h carbon tetrachloride_High High carbon tetrachloride Steatotic_2h_High Steatotic_2h_High Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 7500.00 micromolar 2 hour
003016018018.CEL TG_hum_vit_Ctc_7500um_8h_1 Steatotic Steatotic Steatotic_High high Steatotic_8h carbon tetrachloride_High High carbon tetrachloride Steatotic_8h_High Steatotic_8h_High Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 7500.00 micromolar 8 hour
003016018019.CEL TG_hum_vit_Ctc_7500um_8h_2 Steatotic Steatotic Steatotic_High high Steatotic_8h carbon tetrachloride_High High carbon tetrachloride Steatotic_8h_High Steatotic_8h_High Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 7500.00 micromolar 8 hour
003016018026.CEL TG_hum_vit_Ctc_7500um_24h_1 Steatotic Steatotic Steatotic_High high Steatotic_24h carbon tetrachloride_High High carbon tetrachloride Steatotic_24h_High Steatotic_24h_High Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 7500.00 micromolar 24 hour
003016018027.CEL TG_hum_vit_Ctc_7500um_24h_2 Steatotic Steatotic Steatotic_High high Steatotic_24h carbon tetrachloride_High High carbon tetrachloride Steatotic_24h_High Steatotic_24h_High Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 7500.00 micromolar 24 hour
003016075024.CEL TG_hum_vit_Col_ctl_8h_1 Non_Steatotic Non_steatotic Non_Steatotic_Control none Non_steatotic_8h colchicine_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016075025.CEL TG_hum_vit_Col_ctl_8h_2 Non_Steatotic Non_steatotic Non_Steatotic_Control none Non_steatotic_8h colchicine_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016075030.CEL TG_hum_vit_Col_ctl_24h_1 Non_Steatotic Non_steatotic Non_Steatotic_Control none Non_steatotic_24h colchicine_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016076030.CEL TG_hum_vit_Col_ctl_24h_2 Non_Steatotic Non_steatotic Non_Steatotic_Control none Non_steatotic_24h colchicine_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016075026.CEL TG_hum_vit_Col_800um_8h_1 Non_Steatotic Non_steatotic Non_Steatotic_Middle none Non_steatotic_8h colchicine_Middle Middle colchicine Non_steatotic_8h_Middle Non_steatotic_8h_Control Non_steatotic_8h_MiddleHigh Non_steatotic_8h_Control 800.00 micromolar 8 hour
003016075027.CEL TG_hum_vit_Col_800um_8h_2 Non_Steatotic Non_steatotic Non_Steatotic_Middle none Non_steatotic_8h colchicine_Middle Middle colchicine Non_steatotic_8h_Middle Non_steatotic_8h_Control Non_steatotic_8h_MiddleHigh Non_steatotic_8h_Control 800.00 micromolar 8 hour
003016076002.CEL TG_hum_vit_Col_800um_24h_1 Non_Steatotic Non_steatotic Non_Steatotic_Middle none Non_steatotic_24h colchicine_Middle Middle colchicine Non_steatotic_24h_Middle Non_steatotic_24h_Control Non_steatotic_24h_MiddleHigh Non_steatotic_24h_Control 800.00 micromolar 24 hour
003016076003.CEL TG_hum_vit_Col_800um_24h_2 Non_Steatotic Non_steatotic Non_Steatotic_Middle none Non_steatotic_24h colchicine_Middle Middle colchicine Non_steatotic_24h_Middle Non_steatotic_24h_Control Non_steatotic_24h_MiddleHigh Non_steatotic_24h_Control 800.00 micromolar 24 hour
003016075028.CEL TG_hum_vit_Col_4000um_8h_1 Non_Steatotic Non_steatotic Non_Steatotic_High none Non_steatotic_8h colchicine_High High colchicine Non_steatotic_8h_High Non_steatotic_8h_Control Non_steatotic_8h_MiddleHigh Non_steatotic_8h_Control 4000.00 micromolar 8 hour
003016075029.CEL TG_hum_vit_Col_4000um_8h_2 Non_Steatotic Non_steatotic Non_Steatotic_High none Non_steatotic_8h colchicine_High High colchicine Non_steatotic_8h_High Non_steatotic_8h_Control Non_steatotic_8h_MiddleHigh Non_steatotic_8h_Control 4000.00 micromolar 8 hour
003016076004.CEL TG_hum_vit_Col_4000um_24h_1 Non_Steatotic Non_steatotic Non_Steatotic_High none Non_steatotic_24h colchicine_High High colchicine Non_steatotic_24h_High Non_steatotic_24h_Control Non_steatotic_24h_MiddleHigh Non_steatotic_24h_Control 4000.00 micromolar 24 hour
003016076005.CEL TG_hum_vit_Col_4000um_24h_2 Non_Steatotic Non_steatotic Non_Steatotic_High none Non_steatotic_24h colchicine_High High colchicine Non_steatotic_24h_High Non_steatotic_24h_Control Non_steatotic_24h_MiddleHigh Non_steatotic_24h_Control 4000.00 micromolar 24 hour
003016065008.CEL TG_hum_vit_Imi_ctl_8h_1 Non_Steatotic Non_steatotic Non_Steatotic_Control none Non_steatotic_8h imipramine_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016065009.CEL TG_hum_vit_Imi_ctl_8h_2 Non_Steatotic Non_steatotic Non_Steatotic_Control none Non_steatotic_8h imipramine_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016065014.CEL TG_hum_vit_Imi_ctl_24h_1 Non_Steatotic Non_steatotic Non_Steatotic_Control none Non_steatotic_24h imipramine_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016065015.CEL TG_hum_vit_Imi_ctl_24h_2 Non_Steatotic Non_steatotic Non_Steatotic_Control none Non_steatotic_24h imipramine_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016065010.CEL TG_hum_vit_Imi_3um_8h_1 Non_Steatotic Non_steatotic Non_Steatotic_Middle none Non_steatotic_8h imipramine_Middle Middle imipramine Non_steatotic_8h_Middle Non_steatotic_8h_Control Non_steatotic_8h_MiddleHigh Non_steatotic_8h_Control 3.00 micromolar 8 hour
003016065011.CEL TG_hum_vit_Imi_3um_8h_2 Non_Steatotic Non_steatotic Non_Steatotic_Middle none Non_steatotic_8h imipramine_Middle Middle imipramine Non_steatotic_8h_Middle Non_steatotic_8h_Control Non_steatotic_8h_MiddleHigh Non_steatotic_8h_Control 3.00 micromolar 8 hour
003016065016.CEL TG_hum_vit_Imi_3um_24h_1 Non_Steatotic Non_steatotic Non_Steatotic_Middle none Non_steatotic_24h imipramine_Middle Middle imipramine Non_steatotic_24h_Middle Non_steatotic_24h_Control Non_steatotic_24h_MiddleHigh Non_steatotic_24h_Control 3.00 micromolar 24 hour
003016065017.CEL TG_hum_vit_Imi_3um_24h_2 Non_Steatotic Non_steatotic Non_Steatotic_Middle none Non_steatotic_24h imipramine_Middle Middle imipramine Non_steatotic_24h_Middle Non_steatotic_24h_Control Non_steatotic_24h_MiddleHigh Non_steatotic_24h_Control 3.00 micromolar 24 hour
003016065012.CEL TG_hum_vit_Imi_15um_8h_1 Non_Steatotic Non_steatotic Non_Steatotic_High none Non_steatotic_8h imipramine_High High imipramine Non_steatotic_8h_High Non_steatotic_8h_Control Non_steatotic_8h_MiddleHigh Non_steatotic_8h_Control 15.00 micromolar 8 hour
003016065013.CEL TG_hum_vit_Imi_15um_8h_2 Non_Steatotic Non_steatotic Non_Steatotic_High none Non_steatotic_8h imipramine_High High imipramine Non_steatotic_8h_High Non_steatotic_8h_Control Non_steatotic_8h_MiddleHigh Non_steatotic_8h_Control 15.00 micromolar 8 hour
003016065018.CEL TG_hum_vit_Imi_15um_24h_1 Non_Steatotic Non_steatotic Non_Steatotic_High none Non_steatotic_24h imipramine_High High imipramine Non_steatotic_24h_High Non_steatotic_24h_Control Non_steatotic_24h_MiddleHigh Non_steatotic_24h_Control 15.00 micromolar 24 hour
003016065019.CEL TG_hum_vit_Imi_15um_24h_2 Non_Steatotic Non_steatotic Non_Steatotic_High none Non_steatotic_24h imipramine_High High imipramine Non_steatotic_24h_High Non_steatotic_24h_Control Non_steatotic_24h_MiddleHigh Non_steatotic_24h_Control 15.00 micromolar 24 hour
003016060014.CEL TG_hum_vit_Tam_ctl_8h_1 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_8h tamoxifen_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016060015.CEL TG_hum_vit_Tam_ctl_8h_2 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_8h tamoxifen_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016060020.CEL TG_hum_vit_Tam_ctl_24h_1 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_24h tamoxifen_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016060021.CEL TG_hum_vit_Tam_ctl_24h_2 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_24h tamoxifen_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016060016.CEL TG_hum_vit_Tam_5um_8h_1 Steatotic Steatotic Steatotic_Middle middle Steatotic_8h tamoxifen_Middle Middle tamoxifen Steatotic_8h_Middle Steatotic_8h_Middle Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 5.00 micromolar 8 hour
003016060017.CEL TG_hum_vit_Tam_5um_8h_2 Steatotic Steatotic Steatotic_Middle middle Steatotic_8h tamoxifen_Middle Middle tamoxifen Steatotic_8h_Middle Steatotic_8h_Middle Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 5.00 micromolar 8 hour
003016060022.CEL TG_hum_vit_Tam_5um_24h_1 Steatotic Steatotic Steatotic_Middle middle Steatotic_24h tamoxifen_Middle Middle tamoxifen Steatotic_24h_Middle Steatotic_24h_Middle Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 5.00 micromolar 24 hour
003016060023.CEL TG_hum_vit_Tam_5um_24h_2 Steatotic Steatotic Steatotic_Middle middle Steatotic_24h tamoxifen_Middle Middle tamoxifen Steatotic_24h_Middle Steatotic_24h_Middle Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 5.00 micromolar 24 hour
003016060018.CEL TG_hum_vit_Tam_25um_8h_1 Steatotic Steatotic Steatotic_High high Steatotic_8h tamoxifen_High High tamoxifen Steatotic_8h_High Steatotic_8h_High Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 25.00 micromolar 8 hour
003016060019.CEL TG_hum_vit_Tam_25um_8h_2 Steatotic Steatotic Steatotic_High high Steatotic_8h tamoxifen_High High tamoxifen Steatotic_8h_High Steatotic_8h_High Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 25.00 micromolar 8 hour
003016060024.CEL TG_hum_vit_Tam_25um_24h_1 Steatotic Steatotic Steatotic_High high Steatotic_24h tamoxifen_High High tamoxifen Steatotic_24h_High Steatotic_24h_High Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 25.00 micromolar 24 hour
003016060025.CEL TG_hum_vit_Tam_25um_24h_2 Steatotic Steatotic Steatotic_High high Steatotic_24h tamoxifen_High High tamoxifen Steatotic_24h_High Steatotic_24h_High Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 25.00 micromolar 24 hour
003016037018.CEL TG_hum_vit_Vpa_ctl_2h_1 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_2h valproic acid_Control Control none Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control NA 2 hour
003016037019.CEL TG_hum_vit_Vpa_ctl_2h_2 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_2h valproic acid_Control Control none Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control Non_steatotic_2h_Control NA 2 hour
003016037026.CEL TG_hum_vit_Vpa_ctl_8h_1 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_8h valproic acid_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016037027.CEL TG_hum_vit_Vpa_ctl_8h_2 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_8h valproic acid_Control Control none Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control Non_steatotic_8h_Control NA 8 hour
003016038004.CEL TG_hum_vit_Vpa_ctl_24h_1 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_24h valproic acid_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016038005.CEL TG_hum_vit_Vpa_ctl_24h_2 Steatotic Non_steatotic Steatotic_Control none Non_steatotic_24h valproic acid_Control Control none Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control Non_steatotic_24h_Control NA 24 hour
003016037020.CEL TG_hum_vit_Vpa_200um_2h_1 Steatotic Steatotic Steatotic_Low low Steatotic_2h valproic acid_Low Low valproic acid Steatotic_2h_Low Steatotic_2h_Low Steatotic_2h_Low 200.00 micromolar 2 hour
003016037021.CEL TG_hum_vit_Vpa_200um_2h_2 Steatotic Steatotic Steatotic_Low low Steatotic_2h valproic acid_Low Low valproic acid Steatotic_2h_Low Steatotic_2h_Low Steatotic_2h_Low 200.00 micromolar 2 hour
003016037028.CEL TG_hum_vit_Vpa_200um_8h_1 Steatotic Steatotic Steatotic_Low low Steatotic_8h valproic acid_Low Low valproic acid Steatotic_8h_Low Steatotic_8h_Low Steatotic_8h_Low 200.00 micromolar 8 hour
003016037029.CEL TG_hum_vit_Vpa_200um_8h_2 Steatotic Steatotic Steatotic_Low low Steatotic_8h valproic acid_Low Low valproic acid Steatotic_8h_Low Steatotic_8h_Low Steatotic_8h_Low 200.00 micromolar 8 hour
003016038006.CEL TG_hum_vit_Vpa_200um_24h_1 Steatotic Steatotic Steatotic_Low low Steatotic_24h valproic acid_Low Low valproic acid Steatotic_24h_Low Steatotic_24h_Low Steatotic_24h_Low 200.00 micromolar 24 hour
003016038007.CEL TG_hum_vit_Vpa_200um_24h_2 Steatotic Steatotic Steatotic_Low low Steatotic_24h valproic acid_Low Low valproic acid Steatotic_24h_Low Steatotic_24h_Low Steatotic_24h_Low 200.00 micromolar 24 hour
003016037022.CEL TG_hum_vit_Vpa_1000um_2h_1 Steatotic Steatotic Steatotic_Middle middle Steatotic_2h valproic acid_Middle Middle valproic acid Steatotic_2h_Middle Steatotic_2h_Middle Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 1000.00 micromolar 2 hour
003016037023.CEL TG_hum_vit_Vpa_1000um_2h_2 Steatotic Steatotic Steatotic_Middle middle Steatotic_2h valproic acid_Middle Middle valproic acid Steatotic_2h_Middle Steatotic_2h_Middle Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 1000.00 micromolar 2 hour
003016037030.CEL TG_hum_vit_Vpa_1000um_8h_1 Steatotic Steatotic Steatotic_Middle middle Steatotic_8h valproic acid_Middle Middle valproic acid Steatotic_8h_Middle Steatotic_8h_Middle Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 1000.00 micromolar 8 hour
003016038001.CEL TG_hum_vit_Vpa_1000um_8h_2 Steatotic Steatotic Steatotic_Middle middle Steatotic_8h valproic acid_Middle Middle valproic acid Steatotic_8h_Middle Steatotic_8h_Middle Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 1000.00 micromolar 8 hour
003016038008.CEL TG_hum_vit_Vpa_1000um_24h_1 Steatotic Steatotic Steatotic_Middle middle Steatotic_24h valproic acid_Middle Middle valproic acid Steatotic_24h_Middle Steatotic_24h_Middle Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 1000.00 micromolar 24 hour
003016038009.CEL TG_hum_vit_Vpa_1000um_24h_2 Steatotic Steatotic Steatotic_Middle middle Steatotic_24h valproic acid_Middle Middle valproic acid Steatotic_24h_Middle Steatotic_24h_Middle Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 1000.00 micromolar 24 hour
003016037024.CEL TG_hum_vit_Vpa_5000um_2h_1 Steatotic Steatotic Steatotic_High high Steatotic_2h valproic acid_High High valproic acid Steatotic_2h_High Steatotic_2h_High Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 5000.00 micromolar 2 hour
003016037025.CEL TG_hum_vit_Vpa_5000um_2h_2 Steatotic Steatotic Steatotic_High high Steatotic_2h valproic acid_High High valproic acid Steatotic_2h_High Steatotic_2h_High Steatotic_2h_MiddleHigh Steatotic_2h_MiddleHigh 5000.00 micromolar 2 hour
003016038002.CEL TG_hum_vit_Vpa_5000um_8h_1 Steatotic Steatotic Steatotic_High high Steatotic_8h valproic acid_High High valproic acid Steatotic_8h_High Steatotic_8h_High Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 5000.00 micromolar 8 hour
003016038003.CEL TG_hum_vit_Vpa_5000um_8h_2 Steatotic Steatotic Steatotic_High high Steatotic_8h valproic acid_High High valproic acid Steatotic_8h_High Steatotic_8h_High Steatotic_8h_MiddleHigh Steatotic_8h_MiddleHigh 5000.00 micromolar 8 hour
003016038010.CEL TG_hum_vit_Vpa_5000um_24h_1 Steatotic Steatotic Steatotic_High high Steatotic_24h valproic acid_High High valproic acid Steatotic_24h_High Steatotic_24h_High Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 5000.00 micromolar 24 hour
003016038011.CEL TG_hum_vit_Vpa_5000um_24h_2 Steatotic Steatotic Steatotic_High high Steatotic_24h valproic acid_High High valproic acid Steatotic_24h_High Steatotic_24h_High Steatotic_24h_MiddleHigh Steatotic_24h_MiddleHigh 5000.00 micromolar 24 hour
# Set input parameters         
cutOffAdj.P.Val <- 0.05
cutOfflogFC <- 0
cutOffAveExpr <- 6
cutOffPval <- 0.05 #used if Adj.P.Val removes all

# Groups to compare
Description_column<-"Group"
InterestGroup<- "Steatotic"
Controls<-"Non_steatotic"
Subset input tables. Only include data relevant to current analysis
# remove unused metadata
descriptionTable2<-descriptionTable[,c("Array", "Name", Description_column)]
write.table(descriptionTable2, paste0(descriptionFile, "_sub.txt"), row.names=FALSE, quote=FALSE, sep="\t")

# remove unused samples
descriptionTable2<- descriptionTable2[c(grep(InterestGroup,descriptionTable2[,Description_column]), grep(Controls,descriptionTable2[,Description_column])),]
colnames(descriptionTable2)<-c("Array", "Name", "experimentFactor")
normDataTable<-normDataTable[,c(descriptionTable2$Name)]
Amount of samples per group
Var1 Freq
Non_steatotic 46
Steatotic 62
PCA plot to exclude the post-processing outliers replicates

Creating UMAP plots

Data structuring & cleaning

Statistical analysis with limma

## --[[ Saving table for contrast Steatoticx1+Non_steatoticx-1 ]]--
Displaying top 6 genes, to check data & pipeline correctness

Plotting histograms

## [1] "p-value histograms"
## --[[ Saving Steatoticx1+Non_steatoticx-1.txt P.Value_hist.png ]]--

## [1] "adapted fold change histograms"
## --[[ Saving Steatoticx1+Non_steatoticx-1.txt FC_hist.png ]]--

Creating table based on the cut-offs

## [1] "Creating table based on the cut-offs"
## [1] "Applying cutOffAveExpr (6) removed 11642 genes. 8272 genes remain."
## [1] "Additionally, applying cutOfflogFC (0) removed 0 genes. 8272 genes remain."
## [1] "Additionally, applying cutOffAdj.P.Val (0.05) removed 5125 genes. 3147 genes remain."
## --[[ Saving table Steatoticx1+Non_steatoticx-1_chosen_cutOff.txt ]]--

Creating UMAP based on DEGs

Creating UMAP plots

List of differentially expressed genes (DEGs)

## R version 4.3.1 (2023-06-16 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
## 
## Matrix products: default
## 
## 
## locale:
## [1] LC_COLLATE=Dutch_Netherlands.utf8  LC_CTYPE=Dutch_Netherlands.utf8   
## [3] LC_MONETARY=Dutch_Netherlands.utf8 LC_NUMERIC=C                      
## [5] LC_TIME=Dutch_Netherlands.utf8    
## 
## time zone: Europe/Amsterdam
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] gdata_3.0.0   limma_3.56.2  umap_0.2.10.0 plotly_4.10.3 ggplot2_3.4.4
## [6] DT_0.30       knitr_1.45   
## 
## loaded via a namespace (and not attached):
##  [1] sass_0.4.7        utf8_1.2.4        generics_0.1.3    tidyr_1.3.0      
##  [5] gtools_3.9.4      lattice_0.21-8    digest_0.6.33     magrittr_2.0.3   
##  [9] evaluate_0.23     grid_4.3.1        fastmap_1.1.1     jsonlite_1.8.7   
## [13] Matrix_1.5-4.1    RSpectra_0.16-1   httr_1.4.7        purrr_1.0.2      
## [17] fansi_1.0.5       crosstalk_1.2.0   viridisLite_0.4.2 scales_1.2.1     
## [21] lazyeval_0.2.2    jquerylib_0.1.4   cli_3.6.1         rlang_1.1.1      
## [25] ellipsis_0.3.2    munsell_0.5.0     yaml_2.3.7        withr_2.5.2      
## [29] cachem_1.0.8      tools_4.3.1       dplyr_1.1.3       colorspace_2.1-0 
## [33] reticulate_1.34.0 vctrs_0.6.4       R6_2.5.1          png_0.1-8        
## [37] lifecycle_1.0.4   htmlwidgets_1.6.2 pkgconfig_2.0.3   pillar_1.9.0     
## [41] bslib_0.5.1       gtable_0.3.4      data.table_1.14.8 glue_1.6.2       
## [45] Rcpp_1.0.11       xfun_0.39         tibble_3.2.1      tidyselect_1.2.0 
## [49] highr_0.10        farver_2.1.1      htmltools_0.5.5   rmarkdown_2.25   
## [53] compiler_4.3.1    askpass_1.2.0     openssl_2.1.1

End of Report